Gene loci information

Transcript annotation

  • This transcript has been annotated as Thioredoxin.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11995 g11995.t1 TSS g11995.t1 20230944 20230944
chr_1 g11995 g11995.t1 isoform g11995.t1 20230993 20232065
chr_1 g11995 g11995.t1 exon g11995.t1.exon1 20230993 20231016
chr_1 g11995 g11995.t1 cds g11995.t1.CDS1 20230993 20231016
chr_1 g11995 g11995.t1 exon g11995.t1.exon2 20231627 20231773
chr_1 g11995 g11995.t1 cds g11995.t1.CDS2 20231627 20231773
chr_1 g11995 g11995.t1 exon g11995.t1.exon3 20231913 20232065
chr_1 g11995 g11995.t1 cds g11995.t1.CDS3 20231913 20232065
chr_1 g11995 g11995.t1 TTS g11995.t1 20232436 20232436

Sequences

>g11995.t1 Gene=g11995 Length=324
ATGGTGTACCTTATTAAGGATAAAGCTGATTTCGATGCACAACTTGAAAAAGCTGGAGAT
CTCTTGGTAATCGTAGATTTCTTCGCAACATGGTGCGGTCCATGTAAGATGATTGCTCCA
AAGCTCGAAGAATTTTCAAACACTTACAGCGATAAAATCGTTGTTGTTAAGGTTGACGTT
GATGAATGCGAAGACTTGGCTGTTCAATACAATATTTCGTCCATGCCTACATTTGTTTTC
ATCAAGAAAGGTCAGCAAATTGATAGTTTTTCCGGCGCCAATGCAGAAAAACTCGAAAAA
TATATTACTCAGCACACATCTTAA

>g11995.t1 Gene=g11995 Length=107
MVYLIKDKADFDAQLEKAGDLLVIVDFFATWCGPCKMIAPKLEEFSNTYSDKIVVVKVDV
DECEDLAVQYNISSMPTFVFIKKGQQIDSFSGANAEKLEKYITQHTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11995.t1 CDD cd02947 TRX_family 9 102 6.36087E-28
7 g11995.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 106 4.7E-37
2 g11995.t1 PANTHER PTHR46115 THIOREDOXIN-LIKE PROTEIN 1 1 107 1.2E-45
8 g11995.t1 PIRSF PIRSF000077 Thioredoxin 1 106 7.2E-35
3 g11995.t1 PRINTS PR00421 Thioredoxin family signature 23 31 4.0E-8
4 g11995.t1 PRINTS PR00421 Thioredoxin family signature 31 40 4.0E-8
5 g11995.t1 PRINTS PR00421 Thioredoxin family signature 71 82 4.0E-8
1 g11995.t1 Pfam PF00085 Thioredoxin 6 103 9.5E-34
10 g11995.t1 ProSitePatterns PS00194 Thioredoxin family active site. 24 42 -
12 g11995.t1 ProSiteProfiles PS51352 Thioredoxin domain profile. 2 107 13.495
6 g11995.t1 SUPERFAMILY SSF52833 Thioredoxin-like 2 105 1.74E-36
11 g11995.t1 TIGRFAM TIGR01068 thioredoxin: thioredoxin 9 105 3.7E-33

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0015035 protein-disulfide reductase activity MF
GO:0006662 glycerol ether metabolic process BP
GO:0045454 cell redox homeostasis BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values